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                    <h3><a id="_0"></a>软件安装与路径添加</h3> 
<p> 在涉及到物种或基因组间差异分析的方法中&#xff0c;LEfSe是目前常见的方法。LEfSe实现的方式主要有在线分析和本地分析&#xff0c;在线分析会受到网络及其他因素影响&#xff0c;因而速度可能极慢。本地分析可基于Windows或Linux系统&#xff0c;调参更加灵活。本文以Windows系统为例&#xff0c;向大家展示如何在自己的本本上运行LEfSe&#xff0c;再也不用去求公司了……<br />  首先&#xff0c;我们要安装好Pyhthon&#xff08;2.7版本&#xff09;和R&#xff08;安装方法不再赘述&#xff09;&#xff0c;然后把软件的安装路径添加到电脑的系统环境变量&#xff0c;如R我是安装在“D:\Rnew\R-3.4.4”&#xff0c;那么我复制这个路径&#xff0c;如下图&#xff1a;<br /> <img src="https://img-blog.csdnimg.cn/20190204151342864.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  然后鼠标右击“我的电脑”→“属性”</p> 
<p><img src="https://img-blog.csdnimg.cn/20190204151609591.png" alt="在这里插入图片描述" /><br />  接下来是“高级系统设置”<br /> <img src="https://img-blog.csdnimg.cn/20190204151719523.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  接下来是双击“环境变量”<br /> <img src="https://img-blog.csdnimg.cn/20190204151813160.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  然后双击“环境变量”&#xff0c;我们会看到两个“Path”。<br /> <img src="https://img-blog.csdnimg.cn/20190204151956489.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  为保证不出意外&#xff0c;我们分别对两个Path进行操作。以上面窗口的Path为例&#xff0c;双击Path,然后“新建”&#xff08;我的系统为win10,win10以下的系统貌似是直接双击Path就可以操作&#xff09;&#xff0c;然后把R的安装路径粘贴在新建的框内&#xff0c;然后确定&#xff0c;细心的朋友会发现我还把路径“D:\Rnew\R-3.4.4\bin\x64”加入了“环境变量”&#xff0c;是的&#xff0c;我们需要把这两个路径都加入进来。<br /> <img src="https://img-blog.csdnimg.cn/20190204152311130.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  我们检测一下&#xff0c;看R是否成功加入到Path中&#xff0c;我们打开CMD命令行模式&#xff0c;然后输入R→回车键。如下图&#xff0c;说明我们的操作已经成功。<br /> <img src="https://img-blog.csdnimg.cn/20190204153044742.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  接下来是把Python也加进来&#xff0c;操作方法与R一样&#xff0c;<br /> <img src="https://img-blog.csdnimg.cn/20190204153411759.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /></p> 
<p><img src="https://img-blog.csdnimg.cn/20190204153441997.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/20190204153317120.png" alt="在这里插入图片描述" /><br />  同样的&#xff0c;这里在CMD命令行中输入“python”,然后回车键。如下图&#xff0c;说明python添加到Path成功。<br /> <img src="https://img-blog.csdnimg.cn/20190204153617691.png" alt="在这里插入图片描述" /></p> 
<h3><a id="_24"></a>模块与包的安装</h3> 
<p> 上述的操作后&#xff0c;我们已经把Python和R成功加入到Path中&#xff0c;在用这两个做数据分析时&#xff0c;我们要安装别人已经写好的模块与包&#xff08;packages&#xff09;。LEfSe主要以Python运行为主&#xff0c;但要调用到R的几个packages。首先&#xff0c;对于python&#xff0c;我们需要安装“numpy”、“rpy2”与“matplotlib”三个模块&#xff0c;在R中需要安装好几个packages&#xff0c;如mvtnorm、coin等。我们先安装Python的模块&#xff0c;在数据分析过程中提示未找到“packages”时&#xff0c;我们再用R安装对应的packages。下面以numpy模块安装为例&#xff1a;在CMD命令行中运行&#xff1a;</p> 
<pre><code class="prism language-python">pip install D<span class="token punctuation">:</span>\python\numpy<span class="token operator">-</span><span class="token number">1.14</span><span class="token number">.1</span><span class="token operator">-</span>cp27<span class="token operator">-</span>none<span class="token operator">-</span>win_amd64<span class="token punctuation">.</span>whl
</code></pre> 
<p>等待安装完毕&#xff0c;这里可以分别打开3个CMD&#xff0c;分别安装“numpy”、“rpy2”与“matplotlib”&#xff08;对于模块的安装&#xff0c;我这里是把模块下载到电脑上&#xff0c;也可以联网安装&#xff0c;农村不仅路滑&#xff0c;网也不好&#xff0c;所以下载→本地安装&#xff09;。</p> 
<p><img src="https://img-blog.csdnimg.cn/2019020415512337.png" alt="在这里插入图片描述" /><br />  模块安装好后&#xff0c;我们在CMD命令行中输入python&#xff0c;然后回车键&#xff0c;然后输入&#xff1a;</p> 
<pre><code class="prism language-python"><span class="token keyword">import</span> numpy
</code></pre> 
<p>回车键。如下图&#xff0c;说明numpy被成功安装&#xff0c;切记还有rpy2与matplotlib也要安装&#xff01;<br /> <img src="https://img-blog.csdnimg.cn/20190204155600351.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /></p> 
<h3><a id="R_USER_38"></a>这一步非常重要&#xff0c;我们打开系统环境变量&#xff0c;然后&#34;新建&#34;&#xff0c;变量名为“R_USER”&#xff0c;变量值为某一个路径即可&#xff0c;然后“确定”</h3> 
<p><img src="https://img-blog.csdnimg.cn/20190204160037156.png" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/20190204155958155.png" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/20190204160150808.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  至此&#xff0c;准备就绪&#xff0c;我们需要去下载LEfSe分析的代码:<a href="https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial">https://bitbucket.org/nsegata/metaphlan/wiki/MetaPhlAn_Pipelines_Tutorial</a></p> 
<p><img src="https://img-blog.csdnimg.cn/20190205041125278.png" alt="在这里插入图片描述" /><br /> 然后解压如下图的代码&#xff1a;</p> 
<p><img src="https://img-blog.csdnimg.cn/20190204160357407.png" alt="在这里插入图片描述" /><br /> 得到如下文件&#xff1a;<br /> <img src="https://img-blog.csdnimg.cn/20190204160506184.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  到这里前期工作准备得差不多了&#xff0c;我们需要对物种或者基因的数据进行格式整理&#xff1a;第一列为物种名字&#xff0c;第一行为样本重复&#xff08;切记要灵活运用、操作&#xff09;&#xff1a;</p> 
<p><img src="https://img-blog.csdnimg.cn/20190204161000656.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/20190204161057747.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/20190204161204768.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /></p> 
<h3><a id="_56"></a>开始做分析</h3> 
<p> 打开CMD&#xff0c;把运行路径切换到待分析数据所在路径&#xff1a;我的数据在“D:\yingyong”&#xff0c;</p> 
<pre><code class="prism language-python">D<span class="token punctuation">:</span>
cd D<span class="token punctuation">:</span>\yingyong
</code></pre> 
<p>具体操作如下图。<br /> <img src="https://img-blog.csdnimg.cn/20190204161418389.png" alt="在这里插入图片描述" /><br />  代码路径为“D:\lefse”&#xff0c;第一步&#xff1a;</p> 
<pre><code class="prism language-python">D<span class="token punctuation">:</span>\lefse\format_input<span class="token punctuation">.</span>py hh<span class="token punctuation">.</span>txt lefse<span class="token punctuation">.</span><span class="token keyword">in</span><span class="token punctuation">.</span>txt <span class="token operator">-</span>c <span class="token number">1</span> <span class="token operator">-</span>o <span class="token number">100000</span>
</code></pre> 
<p><img src="https://img-blog.csdnimg.cn/20190204161633265.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  第二步:</p> 
<pre><code class="prism language-python">D<span class="token punctuation">:</span>\lefse\run_lefse<span class="token punctuation">.</span>py lefse<span class="token punctuation">.</span><span class="token keyword">in</span><span class="token punctuation">.</span>txt lefse<span class="token punctuation">.</span>out<span class="token punctuation">.</span>txt <span class="token operator">-</span>l <span class="token number">3</span>
</code></pre> 
<p><img src="https://img-blog.csdnimg.cn/20190204162305192.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  第三步&#xff1a;开始画图&#xff0c;</p> 
<pre><code class="prism language-python">D<span class="token punctuation">:</span>\lefse\plot_res<span class="token punctuation">.</span>py lefse<span class="token punctuation">.</span>out<span class="token punctuation">.</span>txt lda<span class="token punctuation">.</span>pdf <span class="token operator">-</span><span class="token operator">-</span><span class="token builtin">format</span> pdf
</code></pre> 
<p><img src="https://img-blog.csdnimg.cn/20190204162550709.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/20190204162640407.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/20190204162731748.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  第四步&#xff1a;还是图&#xff0c;</p> 
<pre><code class="prism language-python">D<span class="token punctuation">:</span>\lefse\plot_cladogram<span class="token punctuation">.</span>py lefse<span class="token punctuation">.</span>out<span class="token punctuation">.</span>txt yuan<span class="token punctuation">.</span>pdf <span class="token operator">-</span><span class="token operator">-</span><span class="token builtin">format</span> pdf <span class="token operator">-</span><span class="token operator">-</span>labeled_start_lev <span class="token number">1</span>
</code></pre> 
<p><img src="https://img-blog.csdnimg.cn/20190204163036259.png" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/2019020416305829.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br /> <img src="https://img-blog.csdnimg.cn/20190204163118652.png?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3FxXzM4ODU0NTc2,size_16,color_FFFFFF,t_70" alt="在这里插入图片描述" /><br />  那么&#xff0c;LEfSe分析的常见图已经出来&#xff0c;对于biomarker在每个组中的相对丰度&#xff0c;这里不再演示&#xff0c;算是留个悬念&#xff0c;有需要的朋友可以自行探索或加入文后的QQ群→讨论。<br />  对于上面的图&#xff0c;我们会发现物种名没有完全显示&#xff0c;这里我们推荐用AI软件&#xff08;Adobe Illustrator&#xff09;进行调整&#xff08;是调整&#xff0c;不是修改&#xff01;&#xff09;&#xff0c;对于LEfSe分析操作&#xff0c;需要自己灵活操作&#xff0c;照猫画虎绝对是不行的。对于图的解读可以参考已经发表的诸多papers。为加快初学者分析数据、绘图的速度&#xff0c;我们创建了一个QQ群&#xff1a;335774366。欢迎有兴趣的朋友加入→指导。<br />  2019年了&#xff0c;祝各位朋友&#xff1a;“<strong>猪”事顺利→做一只特立独行的猪</strong>?。<br /> 声明&#xff1a;以上内容仅为作者个人理解&#xff0c;有不对的地方&#xff0c;欢迎指正。</p>
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简介
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报错：
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
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便捷的方法时：

打开我们的cmd命令

输入Python

输入 import sys

输入 print(sys.path)

列表中的第五个将是你的安装路径


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				<div class="desc ellipsis-online ellipsis-online-1">本文更新于2019.11.18

更新了今年的版本号
	在表格中用括号备注了包含的python版本号


Release date
			conda
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			python3.4
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		2015-02-25
			
			
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				<div class="desc ellipsis-online ellipsis-online-1">第5章 数据可视化



5.1 二维绘图



5.1.1 一维数据集

按照给定的x和y值绘图

import matplotlib as mpl
import matplotlib.pyplot as plt
%matplotlib inline  # 如果是在控制台上执行代码，这行如果报错，下面的图片显示一张，关闭后再执行下一张的显示，不然都会画到一张图上
np.random.seed(1...</div>
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#一、安装python
欢迎...</div>
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打开链接如下图，版本会一直更新，选择任意一个适合自己电脑的版本就好

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1）双击运行下载好的 python-3.7.0.exe 文件

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import pandas as pd
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如下：
 a b
0 1 1
1 2 2
2 3 3


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我本来想算几个Int值相加的和，本以为很简单的事情，结果却很悲伤，例：
&gt;&gt;&gt;sum = sum(1,2,3)         #结果很明显出现问题报错
TypeError: sum expected at most 2 arguments, got ...</div>
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                <a class="title text-truncate" target="_blank" href="https://blog.csdn.net/qq_38854576/article/details/86763650#comments_13795461" data-report-click='{"mod":"popu_542","spm":"1001.2101.3001.4231","dest":"https://blog.csdn.net/qq_38854576/article/details/86763650#comments_13795461","ab":"new"}' data-report-view='{"mod":"popu_542","spm":"1001.2101.3001.4231","dest":"https://blog.csdn.net/qq_38854576/article/details/86763650#comments_13795461","ab":"new"}'>Python&amp;R LEfSe 分析</a>
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                    <a href="https://blog.csdn.net/qq_38854576" class="user-name" target="_blank">吴苏: </a>
                    <span class="code-comments">在代码前指定python即可。
[code=python]python D:\lefse\format_input.py hh.txt lefse.in.txt -c 1 -o 100000

[/code]</span>
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                    <a href="https://blog.csdn.net/weixin_45051303" class="user-name" target="_blank">梅梅: </a>
                    <span class="code-comments">可以给下练习数据吗，谢谢</span>
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                <a class="title text-truncate" target="_blank" href="https://blog.csdn.net/qq_38854576/article/details/85551896#comments_12927849" data-report-click='{"mod":"popu_542","spm":"1001.2101.3001.4231","dest":"https://blog.csdn.net/qq_38854576/article/details/85551896#comments_12927849","ab":"new"}' data-report-view='{"mod":"popu_542","spm":"1001.2101.3001.4231","dest":"https://blog.csdn.net/qq_38854576/article/details/85551896#comments_12927849","ab":"new"}'>R、主成分分析（PCA）、ggplot2</a>
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                    <a href="https://blog.csdn.net/qq_38854576" class="user-name" target="_blank">吴苏</a>
                    <span class="reply"> 回复 </span>
                    <span class="code-comments">weixin_49356023: QQ群里有！</span>
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                <p class="comment ellipsis">
                    <a href="https://blog.csdn.net/weixin_49356023" class="user-name" target="_blank">weixin_49356023: </a>
                    <span class="code-comments">您好，不知道您方便提供您的数据吗？刚开始学想用来练习一下，谢谢您</span>
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                    <a href="https://blog.csdn.net/weixin_44613442" class="user-name" target="_blank">weixin_44613442: </a>
                    <span class="code-comments">您好，我按照您的流程做，但是在跑lefse第一步：D:\lefse\format_input.py hh.txt lefse.in.txt -c 1 -o 100000，一回车并没有输出文件，反而将脚本format_input.py 打开了。平时都用服务器，不明白windows的终端这样是咋回事？也没有报错信息&hellip;&hellip;希望能得到您的回复</span>
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